I've been doing the same thing to both skins. I've also done more testing for the past day, but what I've gotten it down to. Its just really weird shit.
I compiled the pyra skin where it refers to the materials in the mythra materials folder. Then I made a copy of the pyra vmt files and put it in the mythra folder. The vmts still refer to the vtfs in the pyra materials folder. Shadow lines are gone.
I compiled the pyra skin where it refers to the materials in the pyra materials folder. And of course the pyra vmt files still refer to the pyra vtf files in the pyra folder. Shadow lines are now there.
Not sure it can be alpha blending, because face and body textures are in dxt1 format, so they shouldnt have any alpha layer. Then again I'm not that much of a pro on that stuff.
I guess in the end of it all, I found a workaround for it, but I'm still wondering what causes this. Blessed folder? or maybe cursed folder? lol